GFF to GTF conversion#

It exists many GFF formats and many GTF formats (see here for a complete review) and many tools to perform the conversion. We will try to see in this review the main differences.

Table of Contents#

Test summary
The GFF file to convert
The converters
AGAT
gffread
GenomeTools
ea-utils
TransDecoder
Kent utils
Feature types in GTF versions

Test summary#

tool	respect GTF format	UTR conserved	attribute conserved	Stop codon removed from CDS	Comment
AGAT	Yes - All (default GTF3)	Yes it converts UTR terms to the appropriate ones according to the GTF version selected.	Yes - All	Yes (Only if the feature is present in the file. If not it is possible to add it via agat_sp_add_start_and_stop.pl)	Can take any GTF GFF as input. The only one keeping comments at the beginning of the file.
gffread	No - They say GTF2.2 but it is not: transcript should be removed; start_codon and stop_codon should stay.	No	No	No
GenomeTools	No - only CDS and exon kept	No	No	No	gene_id and transcript_id get new identifiers.
ea-utils	No - only CDS and exon kept	No	No	No
TransDecoder	No - start and stop codon removed	No	Name only	No	Needs the fasta file for the conversion. Location of the last CDS modified and incorrect
Kent utils	No - gene is missing or transcript is superfluous to be compliant to one of the GTF format	No	No	Yes	Create a new attribute 'gene_name'.

The GFF file to convert#

The test file is a GFF3 file:

##gff-version 3
# This is a test sample
scaffold625 maker   gene    337818  343277  .   +   .   ID=CLUHARG00000005458;Name=TUBB3_2
scaffold625 maker   mRNA    337818  343277  .   +   .   ID=CLUHART00000008717;Parent=CLUHARG00000005458
scaffold625 maker   tss 337916  337918  .   +   .   ID=CLUHART00000008717:tss;Parent=CLUHART00000008717
scaffold625 maker   start_codon 337916  337918  .   +   .   ID=CLUHART00000008717:start;Parent=CLUHART00000008717
scaffold625 maker   CDS 337915  337971  .   +   0   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker   CDS 340733  340841  .   +   0   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker   CDS 341518  341628  .   +   2   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker   CDS 341964  343033  .   +   2   ID=CLUHART00000008717:cds;Parent=CLUHART00000008717
scaffold625 maker   stop_codon  343031  343033  .   +   .   ID=CLUHART00000008717:stop;Parent=CLUHART00000008717
scaffold625 maker   exon    337818  337971  .   +   .   ID=CLUHART00000008717:exon1;Parent=CLUHART00000008717
scaffold625 maker   exon    340733  340841  .   +   .   ID=CLUHART00000008717:exon2;Parent=CLUHART00000008717
scaffold625 maker   exon    341518  341628  .   +   .   ID=CLUHART00000008717:exon3;Parent=CLUHART00000008717
scaffold625 maker   exon    341964  343277  .   +   .   ID=CLUHART00000008717:exon4;Parent=CLUHART00000008717
scaffold625 maker   five_prime_utr  337818  337914  .   +   .   ID=CLUHART00000008717:five_prime_utr;Parent=CLUHART00000008717
scaffold625 maker   three_prime_UTR 343034  343277  .   +   .   ID=CLUHART00000008717:three_prime_utr;Parent=CLUHART00000008717

The converters#

AGAT#

AGAT v0.5.1

agat_convert_sp_gff2gtf.pl --gff 1_test.gff -o 1_test_agat.gtf

##gtf-version 3
##This is a test sample
scaffold625 maker   gene    337818  343277  .   +   .   gene_id "CLUHARG00000005458"; ID "CLUHARG00000005458"; Name "TUBB3_2";
scaffold625 maker   transcript  337818  343277  .   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717"; Parent "CLUHARG00000005458"; original_biotype "mrna";
scaffold625 maker   exon    337818  337971  .   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:exon1"; Parent "CLUHART00000008717";
scaffold625 maker   exon    340733  340841  .   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:exon2"; Parent "CLUHART00000008717";
scaffold625 maker   exon    341518  341628  .   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:exon3"; Parent "CLUHART00000008717";
scaffold625 maker   exon    341964  343277  .   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:exon4"; Parent "CLUHART00000008717";
scaffold625 maker   CDS 337915  337971  .   +   0   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:cds"; Parent "CLUHART00000008717";
scaffold625 maker   CDS 340733  340841  .   +   0   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:cds"; Parent "CLUHART00000008717";
scaffold625 maker   CDS 341518  341628  .   +   2   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:cds"; Parent "CLUHART00000008717";
scaffold625 maker   CDS 341964  343030  .   +   2   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:cds"; Parent "CLUHART00000008717";
scaffold625 maker   five_prime_utr  337818  337914  .   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:five_prime_utr"; Parent "CLUHART00000008717";
scaffold625 maker   start_codon 337916  337918  .   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:start"; Parent "CLUHART00000008717";
scaffold625 maker   stop_codon  343031  343033  .   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:stop"; Parent "CLUHART00000008717";
scaffold625 maker   three_prime_utr 343034  343277  .   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; ID "CLUHART00000008717:three_prime_utr"; Parent "CLUHART00000008717"; original_biotype "three_prime_UTR";

gffread#

gffread 0.11.4

gffread -E 1_test.gff -T -o 1_test_gffread.gtf

scaffold625 maker   transcript  337818  343277  .   +   .   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker   exon    337818  337971  .   +   .   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker   exon    340733  340841  .   +   .   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker   exon    341518  341628  .   +   .   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker   exon    341964  343277  .   +   .   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker   CDS 337915  337971  .   +   0   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker   CDS 340733  340841  .   +   0   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker   CDS 341518  341628  .   +   2   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";
scaffold625 maker   CDS 341964  343033  .   +   2   transcript_id "CLUHART00000008717"; gene_id "CLUHARG00000005458";

GenomeTools#

GenomeTools 1.6.1
The help says it convert into GTF2.2

gt gff3_to_gtf 1_test.gff > 1_test_genometools.gtf

scaffold625 maker   exon    337818  337971  .   +   .   gene_id "1"; transcript_id "1.1";
scaffold625 maker   exon    340733  340841  .   +   .   gene_id "1"; transcript_id "1.1";
scaffold625 maker   exon    341518  341628  .   +   .   gene_id "1"; transcript_id "1.1";
scaffold625 maker   exon    341964  343277  .   +   .   gene_id "1"; transcript_id "1.1";
scaffold625 maker   CDS 337915  337971  .   +   0   gene_id "1"; transcript_id "1.1";
scaffold625 maker   CDS 340733  340841  .   +   0   gene_id "1"; transcript_id "1.1";
scaffold625 maker   CDS 341518  341628  .   +   2   gene_id "1"; transcript_id "1.1";
scaffold625 maker   CDS 341964  343033  .   +   2   gene_id "1"; transcript_id "1.1";

ea-utils#

ea-utils commit 2b3d8c5d148801c98a2b3f3d54009a72c5b99521

./gff2gtf-eautils test_1.gff > 1_test_ea-utils.gtf

scaffold625 maker   exon    337818  337971  0   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717:CLUHARG00000005458";
scaffold625 maker   CDS 337915  337971  0   +   0   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717:CLUHARG00000005458";
scaffold625 maker   CDS 340733  340841  0   +   0   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717:CLUHARG00000005458";
scaffold625 maker   exon    340733  340841  0   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717:CLUHARG00000005458";
scaffold625 maker   CDS 341518  341628  0   +   2   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717:CLUHARG00000005458";
scaffold625 maker   exon    341518  341628  0   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717:CLUHARG00000005458";
scaffold625 maker   CDS 341964  343033  0   +   2   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717:CLUHARG00000005458";
scaffold625 maker   exon    341964  343277  0   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717:CLUHARG00000005458";

TransDecoder#

Transdecoder v5.5.0

gff3_gene_to_gtf_format.pl test_1.gff test_1.fa > 1_test_transdecoder.gtf

scaffold625 maker   gene    337818  343277  0   +   .   gene_id "CLUHARG00000005458"; Name "TUBB3_2";
scaffold625 maker   transcript  337818  343277  0   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";
scaffold625 maker   exon    337818  337971  0   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";
scaffold625 maker   CDS 337818  337971  0   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";
scaffold625 maker   exon    340733  340841  0   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";
scaffold625 maker   CDS 340733  340841  0   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";
scaffold625 maker   exon    341518  341628  0   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";
scaffold625 maker   CDS 341518  341628  0   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";
scaffold625 maker   exon    341964  343277  0   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";
scaffold625 maker   CDS 341964  343277  0   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; Name "TUBB3_2";

Kent utils#

version from 26-Feb-2020

./gff3ToGenePred.dms 1_test.gff temp.genePred ./genePredToGtf.dms file temp.genePred 1_test_genePred.gtf

scaffold625 temp.genePred   transcript  337818  343277  .   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717";  gene_name "CLUHARG00000005458";
scaffold625 temp.genePred   exon    337818  337971  .   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "1"; exon_id "CLUHART00000008717.1"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred   CDS 337915  337971  .   +   0   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "1"; exon_id "CLUHART00000008717.1"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred   exon    340733  340841  .   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "2"; exon_id "CLUHART00000008717.2"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred   CDS 340733  340841  .   +   0   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "2"; exon_id "CLUHART00000008717.2"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred   exon    341518  341628  .   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "3"; exon_id "CLUHART00000008717.3"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred   CDS 341518  341628  .   +   2   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "3"; exon_id "CLUHART00000008717.3"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred   exon    341964  343277  .   +   .   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "4"; exon_id "CLUHART00000008717.4"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred   CDS 341964  343030  .   +   2   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "4"; exon_id "CLUHART00000008717.4"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred   start_codon 337915  337917  .   +   0   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "1"; exon_id "CLUHART00000008717.1"; gene_name "CLUHARG00000005458";
scaffold625 temp.genePred   stop_codon  343031  343033  .   +   0   gene_id "CLUHARG00000005458"; transcript_id "CLUHART00000008717"; exon_number "4"; exon_id "CLUHART00000008717.4"; gene_name "CLUHARG00000005458";

Feature types in GTF versions#

GTF version	feature type accepted
GTF3	gene, transcript, exon, CDS, Selenocysteine, start_codon, stop_codon, three_prime_utr, five_prime_utr
GTF2_5	gene, transcript, exon, CDS, UTR, start_codon, stop_codon, Selenocysteine
GTF2_2	CDS, start_codon, stop_codon, 5UTR, 3UTR, inter, inter_CNS, intron_CNS, exon
GTF2_1	CDS, start_codon, stop_codon, exon, 5UTR, 3UTR
GTF2	CDS, start_codon, stop_codon, exon
GTF1	CDS, start_codon, stop_codon, exon, intron